This function allows you to creat a plot of -log10(P-values).

mirrorPlotRACER(assoc_data1, assoc_data2, chr, build = "hg19",
  set = "protein_coding", name1 = "Association Dataset #1",
  name2 = "Association Dataset #2", plotby, gene_plot = NULL,
  snp_plot = NULL, start_plot = NULL, end_plot = NULL)

Arguments

assoc_data1

required. A dataframe that has columns named POS representing the position of the snp on the chromosome, LOG10P which contains the -log10(P-values), CHR, which contains the chromosome number, RS_ID, which LD information. If no column named LD is in the input, LD will be calculated from 1000 genomes phase III in relation to snp_ld_1

assoc_data2

required. identifcal in format to assoc_data1

chr

required. chromosome you wish to plot

build

optional. indicates the genome build to use to plot the genes below the association plot. default = "hg19", but can be changed to "hg38"

set

optional. default = "protein_coding", however can be set to "all" to plot all RNAs in the genome

name1

optional. name of association set 1

name2

optional. name of association set 2

plotby

required. "coord", "gene", or "snp". Which parameter to use to determine the reigon to be plotted.

gene_plot

optional. If "gene" selected for plotby, then plot will be +/- 50kb of gene, should be a human gene symbol

snp_plot

optional. If "snp" selected for plotby, then plot will be +/- 50kb of snp

start_plot

optional. If "coord" selected for plotby, then this will be lower bound of x axis

end_plot

optional. If "coord" selected for plotby, then this will be upper bound of x axis

Examples

# NOT RUN {
data(mark3_bmd_gwas)
data(mark3_eqtl)

mark3_bmd_gwas_f = RACER::formatRACER(assoc_data = mark3_bmd_gwas, chr_col = 3,
pos_col = 4, p_col = 11)
mark3_eqtl_f = RACER::formatRACER(assoc_data = mark3_eqtl, chr_col = 10,
pos_col = 11, p_col = 7)

mark3_bmd_gwas_f_ld = RACER::ldRACER(assoc_data = mark3_bmd_gwas_f,
rs_col = 2, pops ="EUR", lead_snp = "rs11623869")
mark3_eqtl_f_ld = RACER::ldRACER(assoc_data = mark3_eqtl_f,
rs_col = 15, pops = "EUR", lead_snp = "rs11623869")
mirrorPlotRACER(assoc_data1 = mark3_bmd_gwas_f_ld, assoc_data2 = mark3_eqtl_f_ld,
chr = 14, plotby = "gene", gene_plot = "MARK3")
# }